1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
|
// Copyright (C) 1999-2002 Paul O. Lewis
//
// This file is part of NCL (Nexus Class Library).
//
// NCL is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// NCL is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with NCL; if not, write to the Free Software Foundation, Inc.,
// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
#include "ncl/ncl.h"
// not used in rncl/phylobase
#if 0
/*----------------------------------------------------------------------------------------------------------------------
| Sets the base class data member `id' to the name of the block (i.e. "EMPTY") in NEXUS data files.
*/
NxsEmptyBlock::NxsEmptyBlock()
{
id = "EMPTY";
}
/*----------------------------------------------------------------------------------------------------------------------
| Nothing needs to be done.
*/
NxsEmptyBlock::~NxsEmptyBlock()
{
}
/*----------------------------------------------------------------------------------------------------------------------
| The code here is identical to the base class version (simply returns 0), so the code here should either be modified
| or this derived version eliminated altogether. Under what circumstances would you need to modify the default code,
| you ask? This function should be modified to something meaningful if this derived class needs to construct and run
| a NxsSetReader object to read a set involving characters. The NxsSetReader object may need to use this function to
| look up a character label encountered in the set. A class that overrides this method should return the character
| index in the range [1..`nchar']; i.e., add one to the 0-offset index.
*/
unsigned NxsEmptyBlock::CharLabelToNumber(
NxsString s) /* the character label to be translated to character number */
{
return 0;
}
/*----------------------------------------------------------------------------------------------------------------------
| Called when the END or ENDBLOCK command needs to be parsed from within the EMPTY block. Basically just checks to
| make sure the next token in the data file is a semicolon.
*/
void NxsEmptyBlock::HandleEndblock(
NxsToken &token) /* the token used to read from `in' */
{
DemandEndSemicolon(token, "END or ENDBLOCK");
}
/*----------------------------------------------------------------------------------------------------------------------
| This function provides the ability to read everything following the block name (which is read by the NxsReader
| object) to the END or ENDBLOCK statement. Characters are read from the input stream `in'. Overrides the pure
| virtual function in the base class.
*/
void NxsEmptyBlock::Read(
NxsToken &token) /* the token used to read from `in'*/
{
isEmpty = false;
NxsString s;
s = "BEGIN "
s += id;
DemandEndSemicolon(token, s.c_str());
for(;;)
{
token.GetNextToken();
if (token.Equals("END"))
{
HandleEndblock(token);
break;
}
else if(token.Equals("ENDBLOCK"))
{
HandleEndblock(token);
break;
}
else
{
SkippingCommand(token.GetToken());
do
{
token.GetNextToken();
}
while (!token.AtEOF() && !token.Equals(";"));
if (token.AtEOF())
{
errormsg = "Unexpected end of file encountered";
throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
}
}
}
}
/*----------------------------------------------------------------------------------------------------------------------
| Sets `isEmpty' to true in preparation for reading a new EMPTY block. Overrides the pure virtual function in the
| base class.
*/
void NxsEmptyBlock::Reset()
{
NxsBlock::Reset();
}
/*----------------------------------------------------------------------------------------------------------------------
| This function outputs a brief report of the contents of this EMPTY block. Overrides the pure virtual function in
| the base class.
*/
void NxsEmptyBlock::Report(
ostream &out) /* the output stream to which to write the report */
{
out << endl;
out << id << " block contains...";
}
/*----------------------------------------------------------------------------------------------------------------------
| This function is called when an unknown command named `commandName' is about to be skipped. This version of the
| function (which is identical to the base class version) does nothing (i.e., no warning is issued that a command
| was unrecognized). Modify this virtual function to provide such warnings to the user (or eliminate it altogether
| since the base class version already does what this does).
*/
void NxsEmptyBlock::SkippingCommand(
NxsString commandName) /* the name of the command being skipped */
{
}
/*----------------------------------------------------------------------------------------------------------------------
| The code here is identical to the base class version (simply returns 0), so the code here should either be modified
| or this derived version eliminated altogether. Under what circumstances would you need to modify the default code,
| you ask? This function should be modified to something meaningful if this derived class needs to construct and run
| a NxsSetReader object to read a set involving taxa. The NxsSetReader object may need to use this function to look
| up a taxon label encountered in the set. A class that overrides this method should return the taxon index in the
| range [1..ntax]; i.e., add one to the 0-offset index.
*/
unsigned NxsEmptyBlock::TaxonLabelToNumber(
NxsString s) /* the taxon label to be translated to a taxon number */
{
return 0;
}
#endif
|
